ROntoTools: R Onto-Tools suite
Version 2.4.0

Suite of tools for functional analysis.

Browse man pages Browse package API and functions Browse package files

AuthorCalin Voichita <calin@wayne.edu> and Sahar Ansari <saharansari@wayne.edu> and Sorin Draghici <sorin@wayne.edu>
Bioconductor views GraphsAndNetworks Microarray NetworkAnalysis
Date of publicationNone
MaintainerCalin Voichita <calin@wayne.edu>
LicenseCC BY-NC-ND 4.0 + file LICENSE
Version2.4.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ROntoTools")

Man pages

alpha1MR: Compute alpha weights
alphaMLG: Compute alpha weights
compute.fisher: Combine independent p-values using the Fisher method
compute.normalInv: Combine independent p-values using the normal inversion...
KEGGpathway2Graph: Modified version of the same function from KEGGgraph
keggPathwayGraphs: Download and parse KEGG pathway data
keggPathwayNames: Obtain KEGG pathway titles
nodeWeights: Retrieve the node weights of a graph
pDis: Primary dis-regulation: Pathway analysis approach based on...
pDisPathway-class: Class that encodes the result of pDis analysis for a single...
pDisRes-class: Primary dis-regulation (pDis) result class
pe: Pathway-Express: Pathway analysis of signaling pathways
peEdgeRenderInfo: Extract edge render information from a 'pePathway-class'...
peNodeRenderInfo: Extract node render information from a 'pePathway-class'...
pePathway-class: Class that encodes the result of Pathway-Express for a single...
peRes-class: Pathway-Express result class
plot.pePathway-methods: Plot pathway level statistics
plot.peRes-methods: Plot Pathway-Express result
setEdgeWeights: Set gene weights based on edge type
setNodeWeights: Set node weights
subGraphByNodeType: Modified version of the same function from KEGGgraph
summary.pDisRes: Summarize the results of a primary dis-regulation (pDis)...
Summary-pDisRes-method: Summarize the results of a Pathway-Express analysis
summary.peRes: Summarize the results of a Pathway-Express analysis
Summary-peRes-method: Summarize the results of a Pathway-Express analysis

Functions

KEGGpathway2Graph Man page Source code
Summary,pDisRes-method Man page
Summary,peRes-method Man page
addNames Source code
alpha1MR Man page Source code
alphaMLG Man page Source code
compute.B Source code
compute.B_pDis Source code
compute.bootPV Source code
compute.fisher Man page Source code
compute.inverse Source code
compute.normalInv Man page Source code
compute.pAcc Source code
compute.pORA Source code Source code
compute.pPert Source code
compute.ppDis Source code
get.totalAcc Source code
get.totalAccNorm Source code
get.totalPert Source code
get.totalPertNorm Source code
get.totalpDis Source code
get.totalpDisNorm Source code
graph2ftM Source code
keggPathwayGraphs Man page Source code
keggPathwayNames Man page Source code
loadKEGGpathwayDataREST Source code
nodeWeights Man page
nodeWeights,graph,character-method Man page
nodeWeights,graph,missing-method Man page
nodeWeights,graph,numeric-method Man page
pDis Man page Source code
pDis.boot Source code
pDis.helper Source code
pDisPathway-class Man page
pDisRes-class Man page
pe Man page Source code
pe.boot Source code
peEdgeRenderInfo Man page Source code
peNodeRenderInfo Man page Source code
pePathway-class Man page
peRes-class Man page
pf.helper Source code
plot,pePathway,character-method Man page
plot,pePathway,missing-method Man page
plot,peRes,character-method Man page
plot,peRes,missing-method Man page
setEdgeWeights Man page Source code
setNodeWeights Man page Source code
subGraphByNodeType Man page Source code
summary.pDisRes Man page Source code
summary.peRes Man page Source code

Files

DESCRIPTION
LICENSE
NAMESPACE
NEWS
R
R/AllClasses.R
R/AllGenerics.R
R/Summary-methods.R
R/graphWeights.R
R/keggDataREST.R
R/nodeWeights-methods.R
R/pDisExpress.R
R/pDisPathway-utils.R
R/pathwayExpress.R
R/pePathway-utils.R
R/plot-methods.R
R/renderInfo-methods.R
R/summary.pDisRes.R
R/summary.peRes.R
R/utils.R
build
build/vignette.rds
inst
inst/doc
inst/doc/rontotools.R
inst/doc/rontotools.Rnw
inst/doc/rontotools.pdf
inst/extdata
inst/extdata/E-GEOD-21942.topTable.RData
inst/extdata/KEGGRESTunparsed_hsa.RData
inst/extdata/kpgDefault.RData
inst/unitTests
inst/unitTests/test_alpha.R
inst/unitTests/test_graphWeights.R
inst/unitTests/test_nodeWeights.R
inst/unitTests/test_pe.R
man
man/KEGGpathway2Graph.Rd
man/Summary-pDisRes-method.Rd
man/Summary-peRes-method.Rd
man/alpha1MR.Rd
man/alphaMLG.Rd
man/compute.fisher.Rd
man/compute.normalInv.Rd
man/keggPathwayGraphs.Rd
man/keggPathwayNames.Rd
man/nodeWeights.Rd
man/pDis.Rd
man/pDisPathway-class.Rd
man/pDisRes-class.Rd
man/pe.Rd
man/peEdgeRenderInfo.Rd
man/peNodeRenderInfo.Rd
man/pePathway-class.Rd
man/peRes-class.Rd
man/plot.pePathway-methods.Rd
man/plot.peRes-methods.Rd
man/setEdgeWeights.Rd
man/setNodeWeights.Rd
man/subGraphByNodeType.Rd
man/summary.pDisRes.Rd
man/summary.peRes.Rd
tests
tests/runTests.R
vignettes
vignettes/rontotools.Rnw
vignettes/rontotools.bib
ROntoTools documentation built on May 20, 2017, 10:42 p.m.